All Data is publicly available on Chorus.org or PRIDE ARCHIVE
TITLE: Functional Response of Polar Bacterial Communities under Variable Organic Inputs Revealed with Metaproteomic, 16S rRNA and Organic Compositional Analysis
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD008780
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in revision
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TITLE: Proteomic analysis of coral symbionts exposed to thermal stress: Acropora millipora and Symbiodinium adriaticum
ORGANISM: Acropora millipora
PRIDE ACCESSION NUMBER: PXD011668
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
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TITLE: Competition between microbes during anaerobic oxidation of methane: Bioreactor metaproteomics
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD011642
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
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TITLE: Emiliania Huxleyi exposed to 4 treatments of HHQ
ORGANISM: Emiliania Huxleyi
PRIDE ACCESSION NUMBER: PXD011560
DATA TYPE: DIA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
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TITLE: DDA experiments Emiliania huxleyi exposure to 3 doses of HHQ
ORGANISM: Emiliania Huxleyi
PRIDE ACCESSION NUMBER: PXD011559
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
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TITLE: A Proteomics Approach to the Examination of Proteins in Marine Systems
ORGANISM: Ruegeria pomeroyi
PRIDE ACCESSION NUMBER: PXD006689
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to develop assays to detect bacteria in unfractionated POM. Scientific Reports, 8(1), 9276.
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TITLE: Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD006688
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman, E., May, D.H., Mikan, M., Riffle, M., Frazar, C., Harvey, H.R., Noble, W.S., Nunn, B.L. (2016) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. The ISME Journal doi: 10.1038/ismej.2016.132
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TITLE: Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD006472
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
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TITLE: Multi-stress experiment on Pseudonitzschia multiseries
ORGANISM: Pseudonitzschia multiseries
PRIDE ACCESSION NUMBER: PXD006468
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Boyd, P.W., Dillingham, P.W., McGraw, C.M., Armstrong, E.A., Cornwall, C.E., Feng, Y.y., Hurd, C.L., Gault-Ringold, M., Roleda, M.Y., Timmins-Schiffman, E., Nunn, B.L. (2016). Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change 6, 207-213.
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TITLE: Protein recycling in Bering Sea Algal incubations
ORGANISM: Thalasiosira pseudonana and metaproteome
PRIDE ACCESSION NUMBER: PXD006417
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Moore, E.K., Faux, J., Goodlett, D.R., Harvey, H.R., and Nunn, B.L. 2014. Protein recycling in Bering Sea algal incubations. Marine Ecology Progress Series. 515:45-59.
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TITLE: Proteomics of Colwellia psychrerythraea grown at multiple subzero temperatures
ORGANISM: Colwellia psychrerythraea
PRIDE ACCESSION NUMBER: PXD006274
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Nunn, B.L., Slattery, K.; Cameron, K.A.; Timmins-Schiffman, E.; Junge, K. (2015) Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair. Environmental Microbiology. 111, 9009-9014.
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TITLE: Pacific Oyster Ctenidia Proteomics
ORGANISM: Crassostrea gigas (Pacific oyster) (Crassostrea angulata)
PRIDE ACCESSION NUMBER: PXD000835
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. 2014. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics 2014, 15:951 doi:10.1186/1471-2
164-15-951
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TITLE: Geoduck (Panopea generosa) gonad LC-MS/MS
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD003127
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
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TITLE: Geoduck (Panopea generosa) gonad LC-MS/MS DIA
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD004921
DATA TYPE: DIA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
--
TITLE: SRM of geoduck hemolymph peptides to develop biomarkers
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD011006
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
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DATA TYPE: DDA
PUBLIC: YES
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PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
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ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD008780
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in revision
--
TITLE: Proteomic analysis of coral symbionts exposed to thermal stress: Acropora millipora and Symbiodinium adriaticum
ORGANISM: Acropora millipora
PRIDE ACCESSION NUMBER: PXD011668
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
--
TITLE: Competition between microbes during anaerobic oxidation of methane: Bioreactor metaproteomics
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD011642
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
--
TITLE: Emiliania Huxleyi exposed to 4 treatments of HHQ
ORGANISM: Emiliania Huxleyi
PRIDE ACCESSION NUMBER: PXD011560
DATA TYPE: DIA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
--
TITLE: DDA experiments Emiliania huxleyi exposure to 3 doses of HHQ
ORGANISM: Emiliania Huxleyi
PRIDE ACCESSION NUMBER: PXD011559
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: in progress
--
TITLE: A Proteomics Approach to the Examination of Proteins in Marine Systems
ORGANISM: Ruegeria pomeroyi
PRIDE ACCESSION NUMBER: PXD006689
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to develop assays to detect bacteria in unfractionated POM. Scientific Reports, 8(1), 9276.
--
TITLE: Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD006688
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman, E., May, D.H., Mikan, M., Riffle, M., Frazar, C., Harvey, H.R., Noble, W.S., Nunn, B.L. (2016) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. The ISME Journal doi: 10.1038/ismej.2016.132
--
TITLE: Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics
ORGANISM: metaproteome
PRIDE ACCESSION NUMBER: PXD006472
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
--
TITLE: Multi-stress experiment on Pseudonitzschia multiseries
ORGANISM: Pseudonitzschia multiseries
PRIDE ACCESSION NUMBER: PXD006468
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Boyd, P.W., Dillingham, P.W., McGraw, C.M., Armstrong, E.A., Cornwall, C.E., Feng, Y.y., Hurd, C.L., Gault-Ringold, M., Roleda, M.Y., Timmins-Schiffman, E., Nunn, B.L. (2016). Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change 6, 207-213.
--
TITLE: Protein recycling in Bering Sea Algal incubations
ORGANISM: Thalasiosira pseudonana and metaproteome
PRIDE ACCESSION NUMBER: PXD006417
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Moore, E.K., Faux, J., Goodlett, D.R., Harvey, H.R., and Nunn, B.L. 2014. Protein recycling in Bering Sea algal incubations. Marine Ecology Progress Series. 515:45-59.
--
TITLE: Proteomics of Colwellia psychrerythraea grown at multiple subzero temperatures
ORGANISM: Colwellia psychrerythraea
PRIDE ACCESSION NUMBER: PXD006274
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Nunn, B.L., Slattery, K.; Cameron, K.A.; Timmins-Schiffman, E.; Junge, K. (2015) Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair. Environmental Microbiology. 111, 9009-9014.
--
TITLE: Pacific Oyster Ctenidia Proteomics
ORGANISM: Crassostrea gigas (Pacific oyster) (Crassostrea angulata)
PRIDE ACCESSION NUMBER: PXD000835
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. 2014. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics 2014, 15:951 doi:10.1186/1471-2
164-15-951
--
TITLE: Geoduck (Panopea generosa) gonad LC-MS/MS
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD003127
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
--
TITLE: Geoduck (Panopea generosa) gonad LC-MS/MS DIA
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD004921
DATA TYPE: DIA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
--
TITLE: SRM of geoduck hemolymph peptides to develop biomarkers
ORGANISM: Panopea generosa
PRIDE ACCESSION NUMBER: PXD011006
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT: Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation.Journal of Proteome Research, 16(9), pp 3298-3309.
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ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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TITLE:
ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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TITLE:
ORGANISM:
PRIDE ACCESSION NUMBER:
DATA TYPE: DDA
PUBLIC: YES
PUBLISHED MANUSCRIPT:
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